Contacts of the helix formed by residues 70 - 98 (chain F) in PDB entry 5TWV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 70 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F HIS* 5.4 0.6 + - - -
68F PHE* 3.2 0.8 + - - -
69F PRO* 1.3 74.3 - - - +
71F HIS* 1.3 60.8 + - - +
72F ASN 3.4 2.2 - - - -
73F LEU* 3.9 14.0 - - - +
74F ARG* 3.1 29.5 + - - +
124F TYR* 5.7 0.3 - - - -
185F VAL* 5.5 7.1 - - - +
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Residues in contact with HIS 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F LEU 5.1 7.9 - - - -
67F HIS* 3.4 35.5 + + + +
68F PHE* 3.3 26.1 + + + +
70F GLY* 1.3 78.3 - - - +
72F ASN* 1.3 62.1 + - - +
74F ARG* 3.3 7.4 + - + +
75F TRP* 3.3 64.0 + + - +
124F TYR* 5.5 15.2 - + + -
128F GLU* 5.1 12.8 - - + -
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Residues in contact with ASN 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F GLY* 3.4 0.6 - - - -
71F HIS* 1.3 79.1 - - - +
73F LEU* 1.3 57.2 + - - +
74F ARG 3.3 0.2 - - - -
75F TRP* 4.0 12.0 - - + +
76F ILE* 3.3 24.6 + - - +
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Residues in contact with LEU 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F GLY* 3.6 15.5 + - - +
71F HIS 3.2 0.4 - - - -
72F ASN* 1.3 77.9 - - - +
74F ARG* 1.3 59.8 + - - +
75F TRP 3.4 0.7 - - - -
76F ILE* 3.9 7.9 - - - +
77F LEU* 3.2 25.1 + - - +
181F MET* 6.1 0.5 - - - +
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Residues in contact with ARG 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F GLY 3.1 19.6 + - - +
71F HIS* 3.6 9.9 - - + +
72F ASN 3.3 0.2 - - - -
73F LEU* 1.3 79.2 - - - +
75F TRP* 1.3 61.4 + - + +
76F ILE 3.4 0.2 - - - -
77F LEU* 3.7 4.8 + - - +
78F THR* 3.2 25.1 + - - -
124F TYR* 4.1 38.3 - - + +
185F VAL* 5.6 1.6 - - + -
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Residues in contact with TRP 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F HIS* 3.3 51.1 + + - +
72F ASN* 4.3 8.5 - - + +
74F ARG* 1.3 81.0 - - + +
76F ILE* 1.3 58.4 + - - +
77F LEU 3.1 2.0 - - - -
78F THR* 3.2 7.0 + - - -
79F PHE* 3.0 51.6 + + + -
225F LEU 3.0 28.9 - - - -
226F SER* 3.6 29.8 - - - -
227F LYS* 4.5 7.4 - - + -
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Residues in contact with ILE 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F ASN 3.3 18.6 + - - +
73F LEU* 4.3 7.2 - - - +
75F TRP* 1.3 81.9 - - - +
77F LEU* 1.3 55.5 + - - +
79F PHE* 3.9 6.0 - - - +
80F ILE* 3.2 26.3 + - - +
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Residues in contact with LEU 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F LEU 3.2 19.4 + - - +
74F ARG* 3.7 5.4 + - - +
75F TRP 3.1 0.2 - - - -
76F ILE* 1.3 77.7 - - - +
78F THR* 1.3 61.1 + - - +
79F PHE 3.3 1.1 - - - -
80F ILE* 3.9 6.0 - - - +
81F LEU* 3.1 26.9 + - - +
143F TRP* 5.8 7.6 - - + -
178F LEU* 5.3 12.2 - - + +
181F MET* 5.3 14.6 - - + -
182F LEU* 6.0 3.4 - - + +
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Residues in contact with THR 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ARG 3.2 17.4 + - - -
75F TRP* 3.2 14.1 + - - -
77F LEU* 1.3 80.5 - - - +
79F PHE* 1.3 61.8 + - - +
81F LEU* 4.0 5.5 - - - +
82F LEU* 3.8 16.8 + - - +
117F ALA* 5.6 11.9 - - - +
121F VAL* 5.6 9.2 - - - -
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Residues in contact with PHE 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F TRP* 3.0 41.1 + + + +
76F ILE* 4.2 5.8 - - - +
78F THR* 1.3 80.4 - - - +
80F ILE* 1.3 58.4 + - - +
81F LEU 3.2 1.6 - - - -
82F LEU* 3.2 33.3 + - + +
83F PHE* 3.1 32.8 - + + -
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Residues in contact with ILE 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F ILE 3.2 19.6 + - - +
77F LEU* 4.4 4.9 - - - -
79F PHE* 1.3 75.3 - - - +
81F LEU* 1.3 56.6 + - - +
82F LEU 3.1 4.9 - - - -
83F PHE* 3.6 12.3 + - - +
84F VAL* 3.3 23.7 + - - +
178F LEU* 6.4 2.2 - - + -
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Residues in contact with LEU 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F LEU 3.1 20.9 + - - +
78F THR* 4.3 7.0 - - - +
79F PHE 3.2 0.4 - - - -
80F ILE* 1.3 76.4 - - - +
82F LEU* 1.3 58.9 + - - +
83F PHE 3.4 0.2 - - - -
84F VAL* 3.7 8.7 - - - +
85F LEU* 3.1 26.3 + - - +
117F ALA* 5.0 17.6 - - + +
143F TRP* 6.0 5.6 - - + -
178F LEU* 5.3 11.4 - - + -
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Residues in contact with LEU 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F THR 3.8 11.9 + - - +
79F PHE* 3.2 29.5 + - + +
81F LEU* 1.3 78.0 - - - +
83F PHE* 1.3 64.3 - - + +
84F VAL 3.1 1.6 - - - -
85F LEU* 3.2 7.7 + - + +
86F VAL* 3.0 29.1 + - - +
114F PHE* 6.0 6.3 - - + -
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Residues in contact with PHE 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F PHE* 3.1 38.0 + + + -
80F ILE* 3.6 11.2 + - - +
82F LEU* 1.3 86.2 - - + +
84F VAL* 1.3 57.7 + - - +
86F VAL* 3.9 7.6 + - + +
87F CYS* 3.3 24.8 + - - +
361F LEU* 5.7 11.9 - - + -
364F LEU* 5.9 8.3 - - + -
365F ALA* 6.0 9.0 - - + -
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Residues in contact with VAL 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F ILE 3.3 15.3 + - - +
81F LEU* 4.0 8.3 - - - +
82F LEU 3.1 0.4 - - - -
83F PHE* 1.3 79.8 - - - +
85F LEU* 1.3 58.3 + - - +
86F VAL 3.4 0.2 - - - -
87F CYS* 3.9 7.8 - - - +
88F GLU* 3.2 24.8 + - - +
171F LEU* 5.1 8.0 - - - +
174F LEU* 4.6 21.5 - - + +
175F LEU* 4.9 13.0 - - + +
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Residues in contact with LEU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F LEU 3.1 18.4 + - - +
82F LEU* 3.2 10.5 + - + +
84F VAL* 1.3 76.9 - - - +
86F VAL* 1.3 65.3 + - - +
87F CYS 3.3 0.2 - - - -
88F GLU* 4.0 4.4 - - - +
89F ILE* 3.2 31.5 + - + +
110F ALA* 4.6 8.8 - - - +
113F ALA* 5.4 5.8 - - + -
114F PHE* 4.6 25.4 - - + +
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Residues in contact with VAL 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F LEU 3.0 16.8 + - - +
83F PHE* 4.0 9.4 - - + +
85F LEU* 1.3 78.7 - - - +
87F CYS* 1.3 56.3 + - - +
89F ILE* 3.5 6.3 + - - +
90F ALA* 3.0 29.0 + - - +
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Residues in contact with CYS 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F PHE 3.3 17.9 + - - +
84F VAL* 4.0 7.9 - - - +
85F LEU 3.3 0.4 - - - -
86F VAL* 1.3 77.7 - - - +
88F GLU* 1.3 64.8 + - - +
90F ALA* 3.3 7.1 + - - +
91F GLU* 3.1 23.9 + - - +
171F LEU* 4.9 10.8 - - + +
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Residues in contact with GLU 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F VAL 3.2 17.4 + - - +
85F LEU* 4.3 3.1 - - - +
86F VAL 3.4 0.2 - - - -
87F CYS* 1.3 79.7 - - - +
89F ILE* 1.3 58.3 + - - +
91F GLU* 3.4 4.4 + - - +
92F GLY* 2.9 24.3 + - - -
107F TYR* 6.0 0.2 - - - +
110F ALA* 3.7 22.5 - - + +
171F LEU* 4.2 18.3 - - + +
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Residues in contact with ILE 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F LEU* 3.2 22.2 + - + +
86F VAL* 3.5 6.2 + - - +
87F CYS 3.3 0.2 - - - -
88F GLU* 1.3 74.9 - - - +
90F ALA* 1.3 54.7 + - - +
92F GLY* 3.0 2.9 + - - +
93F ILE* 2.7 57.3 + - + +
107F TYR* 5.2 7.6 - - + +
110F ALA* 3.5 32.8 - - + +
111F GLY* 4.6 7.4 - - - +
114F PHE* 5.4 6.1 - - + -
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Residues in contact with ALA 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F VAL 3.0 19.0 + - - +
87F CYS* 3.3 9.4 + - - +
89F ILE* 1.3 79.9 - - - +
91F GLU* 1.3 60.8 + - - +
93F ILE* 3.5 15.7 + - - +
94F LEU* 3.6 10.9 + - - +
354F ASN* 5.6 12.1 - - + +
357F VAL* 5.7 9.2 - - + -
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Residues in contact with GLU 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F CYS 3.1 12.4 + - - +
88F GLU* 3.7 9.6 - - - +
90F ALA* 1.3 74.8 - - - +
92F GLY* 1.3 64.2 + - - +
94F LEU* 3.2 17.7 + - - +
95F SER* 3.3 12.5 + - - -
167F LEU* 4.5 21.1 - - + +
168F ARG* 5.5 2.5 - - - -
171F LEU* 5.8 1.3 - - + -
344F TYR* 4.5 24.2 - - + +
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Residues in contact with GLY 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F GLU 2.9 14.7 + - - -
89F ILE 3.0 5.5 + - - -
91F GLU* 1.3 75.4 - - - +
93F ILE* 1.3 65.2 + - - +
95F SER* 3.3 8.4 + - - -
96F ASP* 3.2 21.5 + - - +
106F LEU* 5.4 3.5 - - - +
107F TYR* 4.3 25.7 - - - +
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Residues in contact with ILE 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F ILE* 2.7 41.4 + - + +
90F ALA* 3.7 10.3 - - - +
91F GLU 3.3 0.4 - - - -
92F GLY* 1.3 72.5 - - - +
94F LEU* 1.3 63.6 + - - +
96F ASP* 3.3 9.6 + - + +
97F GLY* 3.2 18.7 + - - -
107F TYR* 6.0 7.0 - - + -
353F GLY* 6.4 1.6 - - - -
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Residues in contact with LEU 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F ALA 3.6 7.4 + - - +
91F GLU* 3.2 13.5 + - - +
93F ILE* 1.3 81.0 - - - +
95F SER* 1.3 61.7 + - - +
97F GLY* 3.4 9.8 + - - -
98F VAL* 3.5 10.0 + - - +
336F PRO* 4.5 24.2 - - + +
337F LYS* 5.6 2.5 - - + -
344F TYR* 6.1 3.6 - - + -
345F PHE* 4.4 36.3 - - + +
347F SER 5.5 1.3 - - - +
348F SER* 5.4 7.9 - - - +
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Residues in contact with SER 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F GLU 3.3 8.7 + - - -
92F GLY* 3.3 11.6 + - - -
93F ILE 3.3 0.4 - - - -
94F LEU* 1.3 81.3 - - - +
96F ASP* 1.3 62.8 + - - +
97F GLY 3.4 0.2 + - - -
98F VAL* 3.5 18.0 - - - +
103F HIS* 6.0 1.0 - - - +
106F LEU* 4.8 15.6 - - - +
341F LEU 4.9 8.9 + - - -
342F GLY 4.9 6.6 + - - -
343F VAL* 5.2 9.8 - - - -
344F TYR* 5.4 7.8 - - - +
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Residues in contact with ASP 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F GLY 3.2 10.0 + - - +
93F ILE* 3.7 12.1 - - + +
94F LEU 3.3 0.2 - - - -
95F SER* 1.3 80.7 - - - +
97F GLY* 1.3 61.8 + - - +
98F VAL* 3.5 0.7 + - - +
99F THR* 3.9 4.0 + - - -
101F SER 4.2 14.7 - - - +
102F ARG* 4.7 11.2 - - + +
103F HIS* 5.4 7.2 - - - +
106F LEU* 6.3 0.4 - - - +
107F TYR* 4.4 22.9 - - + -
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Residues in contact with GLY 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F ILE 3.2 11.0 + - - -
94F LEU* 3.4 4.2 + - - -
95F SER 3.3 0.4 - - - -
96F ASP* 1.3 76.2 - - - +
98F VAL* 1.3 47.4 - - - +
99F THR* 1.5 44.1 + - - -
336F PRO* 6.0 2.2 - - - -
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Residues in contact with VAL 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F LEU 3.5 10.5 + - - +
95F SER* 3.5 17.0 - - - +
96F ASP 3.4 1.1 - - - +
97F GLY* 1.3 68.6 - - - +
99F THR* 1.3 67.1 + - - +
100F GLU* 3.3 11.8 + - + +
101F SER 5.7 2.5 - - - +
336F PRO* 5.1 19.2 - - - +
341F LEU* 5.0 19.1 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il